python main.py Fig.S3A_Q0238_CBE-3to5_S136_L001_R1_001.fastq.gz out/Fig.S3A_Q0238_CBE-3to5_S136_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0251_CBE-3to5_S139_L001_R1_001.fastq.gz out/Fig.S3A_Q0251_CBE-3to5_S139_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0346_Untreated-3to5_S160_L001_R1_001.fastq.gz out/Fig.S3A_Q0346_Untreated-3to5_S160_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0346_Untreated-3to5_S161_L001_R1_001.fastq.gz out/Fig.S3A_Q0346_Untreated-3to5_S161_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0346_Untreated-5to3_S128_L001_R1_001.fastq.gz out/Fig.S3A_Q0346_Untreated-5to3_S128_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0346_Untreated-5to3_S129_L001_R1_001.fastq.gz out/Fig.S3A_Q0346_Untreated-5to3_S129_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0361_UT-3to5_S163_L001_R1_001.fastq.gz out/Fig.S3A_Q0361_UT-3to5_S163_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0361_UT-3to5_S164_L001_R1_001.fastq.gz out/Fig.S3A_Q0361_UT-3to5_S164_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0361_UT-5to3_S133_L001_R1_001.fastq.gz out/Fig.S3A_Q0361_UT-5to3_S133_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
python main.py Fig.S3A_Q0361_UT-5to3_S132_L001_R1_001.fastq.gz out/Fig.S3A_Q0361_UT-5to3_S132_L001_R1_001 -a CTTCAGGGTCTGTCCCATCGGGCAGGAAGCCGTCATGGCAACCCTGGAAAAGCTGATGAAGGCCTTCGAGTCCCTCAAGTCCTTC(YAR)CAACAGCCGCCACCGCCGCCGCCGCCGCCGCCGCCTCCTCAGCTTCCTCAGCC --no_trim -amas 80
